SARS_COV_2_ORF1AB_ClustalOmega_MView
Reference sequence (1): ORF1AB_China_Dec2019a
Identities normalised by aligned length.
Colored by: identity
                                                cov    pid    1 [        .         .         .         .         :         .         .         .         .         1         .         . 120 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPH------------------ELV--     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS--ARTAPHG-------------HVMVELV--     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-EARTAPHG-------------HVMVELV--     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      ---------------MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS-DARTAPHG-------------HVMVELV--     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLCG--------SGNLVEKL----SPWFMDGENAYEVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQLAY     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLCG--------SGNLVEKL----SPWFMDGENAYEVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQLAY     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLCG--------SGNLVEKL----SPWFMDGENAYEVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQLAY     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      MSFVAGVTAQGARGTYRAALNSEKHQDHVSLTVPLCG--------SGNLVEKL----SPWFMDGENAYEVVKAMLLKKEPLLYVPIRLAGHTRHLPGPRVYLVERLIACENPFMVNQLAY     
   consensus/100%                                               ...............hcuhlsu.pcpsHVpLolPlht.........Gs.VEcl....p.ahhDGpsuh..VcthlL.p....YV.I+hu..sRphPt..................p.l..     
   consensus/90%                                                ...............MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS.cARTAPHs..............hMVELV..     
   consensus/80%                                                ...............MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS.DARTAPHG.............HVMVELV..     
   consensus/70%                                                ...............MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRS.DARTAPHG.............HVMVELV..     

                                                cov    pid  121          .         .         :         .         .         .         .         2         .         .         .         . 240 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADL---DLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      -AELEG--IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      SSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGRGGYHYTPFHYE---------RDNTSCPEWMDDFEADPKGKYAQNLLKKLIGGDV-TPVDQYMCGVDGKPISAYAFLMA     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      SSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGRGGYHYTPFHYE---------RDNTSCPEWMDDFEADPKGKYAQNLLKKLIGGDV-TPVDQYMCGVDGKPISAYAFLMA     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      SSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGRGGYHYTPFHYE---------RDNTSCPEWMDDFEADPKGKYAQNLLKKLIGGDV-TPVDQYMCGVDGKPISAYAFLMA     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      SSSANGSLVGTTLQGKPIGMFFPYDIELVTGKQNILLRKYGRGGYHYTPFHYE---------RDNTSCPEWMDDFEADPKGKYAQNLLKKLIGGDV-TPVDQYMCGVDGKPISAYAFLMA     
   consensus/100%                                               .uphpG..lthshpGcslGhhhPashElssuhpplLLRK.GptGhthpsath-.........hssssh.-a.-sapsc.puthsppLh+cL.GGsh.p.VDp.hCGsDGhPlpsht.LhA     
   consensus/90%                                                .AELEG..IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADL...DLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
   consensus/80%                                                .AELEG..IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     
   consensus/70%                                                .AELEG..IQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLA     

                                                cov    pid  241          :         .         .         .         .         3         .         .         .         .         :         . 360 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      RAGKASCTLS-EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS---VYPVASPNECNQMCLSTLMK     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      KDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPP-HYFTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAFIE     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      KDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPP-HYFTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAFIE     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      KDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPP-HYFTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAFIE     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      KDGITKLADVEADVAARADDEGFITLKNNLYRLVWHVERKDVPYPKQSIFTINSVVQKDGVENTPP-HYFTLGCKILTLTPRNKWSGVSDLSLKQKLLYTFYGKESLENPTYIYHSAFIE     
   consensus/100%                                               +sGhsphs.s.tplshhssccGhhsh+pp.aclsWasERp-hsY.hQo.FpIp.shphDshpspsP.ahFsLsshIhTlpPRschptlssh.h+.+....hYshtS.ppss.hhhSshhc     
   consensus/90%                                                RAGKASCTLS.EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS...VYPVASPNECNQMCLSTLMK     
   consensus/80%                                                RAGKASCTLS.EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS...VYPVASPNECNQMCLSTLMK     
   consensus/70%                                                RAGKASCTLS.EQLDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFPLNSIIKTIQPRVEKKKLDGFMGRIRS...VYPVASPNECNQMCLSTLMK     

                                                cov    pid  361          .         .         .         4         .         .         .         .         :         .         .         . 480 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRANANIGCNHT     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      CDHCGETSWQTGDFVKATCEFCGTENLTKE-GATTCGYLPQNAVVKIYCPACHNSEVGP--EHSL---AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      CGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSE-RCNVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGD     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      CGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSE-RCNVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGD     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      CGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSE-RCNVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGD     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      CGSCGNDSWLTGNAIQGFACGCGASYTANDVEVQSSGMIKPNALLCATCPFAKGDSCSSNCKHSVAQLVSYLSE-RCNVIADSKSFTLIFGGVAYAYFGCEEGTMYFVPRAKSVVSRIGD     
   consensus/100%                                               CspCGpsSW.TGshlpuhsphCGsp.hsp-.tsposGhl..NAllphhCPhs+sspsus..cHSl...spYhsE.thpsIhcptuhTlhFGGssauYhGCcptshYaVPRApuslup.ts     
   consensus/90%                                                CDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCPACHNSEVGP..EHSL...AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRAsANIGCNHT     
   consensus/80%                                                CDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCPACHNSEVGP..EHSL...AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     
   consensus/70%                                                CDHCGETSWQTGDFVKATCEFCGTENLTKE.GATTCGYLPQNAVVKIYCPACHNSEVGP..EHSL...AEYHNESGLKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHT     

                                                cov    pid  481          .         5         .         .         .         .         :         .         .         .         .         6 600 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      GVVGEGSEGLND----NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS---ILSPLYAFASEAARV---VRS     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      SIFT-GCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKVAT     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      SIFT-GCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKVAT     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      SIFT-GCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKVAT     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      SIFT-GCTGSWNKVTQIANMFLEQTQHSLNFVGEFVVNDVVLAILSGTTTNVDKIRQLLKGVTLDKLRDYLADY-DVAVTAGPFMDNAINVGGTGLQYAAITAPYVVLTGLGESFKKVAT     
   consensus/100%                                               ulhs.GspG..s.....h..hLpppphslNhVG-FhlN-.lhhILuuhossssthhphlKGlshcth+phltsh.shtVTtG.hhcsAhNlGtpt....hlos.Yshhothucs...Vto     
   consensus/90%                                                GVVGEGSEGLND....NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS...ILSPLYAFASEAARV...VRS     
   consensus/80%                                                GVVGEGSEGLND....NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS...ILSPLYAFASEAARV...VRS     
   consensus/70%                                                GVVGEGSEGLND....NLLEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGNFKVTKGKAKKGAWNIGEQKS...ILSPLYAFASEAARV...VRS     

                                                cov    pid  601          .         .         .         .         :         .         .         .         .         7         .         . 720 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      IFSRTLETAQNSVRV------LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT-----------NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      IPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCVDLSVA--ST-----YFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVY-     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      IPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCVDLSVA--ST-----YFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVY-     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      IPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCVDLSVA--ST-----YFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVY-     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      IPYKVCNSVKDTLTYYAHSVLYRVFPYDMDSGVSSFSELLFDCVDLSVA--ST-----YFLVRLLQDKTGDFMSTIITSCQTAVSKLLDTCFEATEATFNFLLDLAGLFRIFLRNAYVY-     
   consensus/100%                                               I..+shpospsolph......hphhshsh.sGlSpaS.hLhDsh.hoss..os.....halsthl.phTupaho...........plhsTsaEthcsshsaL.-hht.hh.FLRsua.h.     
   consensus/90%                                                IFSRTLETAQNSVRV......LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT...........NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
   consensus/80%                                                IFSRTLETAQNSVRV......LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT...........NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     
   consensus/70%                                                IFSRTLETAQNSVRV......LQKAAITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLT...........NIFGTVYEKLKPVLDWLEEKFKEGVEFLRDGWEIV     

                                                cov    pid  721          .         .         :         .         .         .         .         8         .         .         .         . 840 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN-LGETFVTHSKGLYRKCVK------------------SREETGLLMPLKAPKEIIFLEGETLPTE     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ---TSQGFVVVNGKVSTLV-------KQVLDLLNKGMQLLHTKVSWAGFNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVT--------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ---TSQGFVVVNGKVSTLV-------KQVLDLLNKGMQLLHTKVSWAGSNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVT--------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      ---TSQGFVVVNGKVSTLV-------KQVLDLLNKGMQLLHTKVSWAGSNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVT--------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      ---TSQGFVVVNGKVSTLV-------KQVLDLLNKGMQLLHTKVSWAGFNISAVIYSGRESLIFPSGTYY-CVTTKAKSVQQDLDVILPGEFSKKQLGLLQPTDNSTTVSVT--------     
   consensus/100%                                               ...oopuh.lVsGplsThs.......pphhcLlNKhhtLhtspl.huG.plpAl...Gcp.lhaspGhYh.CVp..................S+cphGLL.Phcssppl.hh........     
   consensus/90%                                                KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN.LGETFVTHSKGLYRKCVK..................SREETGLLMPLKAPKEIIFLEGETLPTE     
   consensus/80%                                                KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN.LGETFVTHSKGLYRKCVK..................SREETGLLMPLKAPKEIIFLEGETLPTE     
   consensus/70%                                                KFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKLKALN.LGETFVTHSKGLYRKCVK..................SREETGLLMPLKAPKEIIFLEGETLPTE     

                                                cov    pid  841          :         .         .         .         .         9         .         .         .         .         :         . 960 
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGSAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY--CALAPNMMVTNNTFTLKGGAPT-KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK-CSAYTVELGT     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      VSSNMVETVVGQL---EQTN-MHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSL     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      VSSNMVETVVGQL---EQTN-MHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSL     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      VSSNMVETVVGQL---EQTN-MHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      VSSNMVETVVGQL---EQTN-MHSPDVIVGDYVIISEKLFVRSKEEDGFAFYPACTNGHAVPTLFRLKGGAPVKKVAFGGDQVHEVAAVRSVTVEYNIHAVLDTLLASSSLRTFVVDKSL     
   consensus/100%                                               V.op.V.hhsGpL...EQss..ts.sslVGs.VhIsthhhlc.K-p-ta..hshssNhhsssshFpLKGuAPs.KVsFGsDpVhEVtuh+SVslpaplcthlDplLspp.hpsasV-huh     
   consensus/90%                                                VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY..CALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK.CSAYTVELGT     
   consensus/80%                                                VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY..CALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK.CSAYTVELGT     
   consensus/70%                                                VLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKY..CALAPNMMVTNNTFTLKGGAPT.KVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK.CSAYTVELGT     

                                                cov    pid  961          .         .         .         0         .         .         .         .         :         .         .         . 1080
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQE-EEQEE--D     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSIATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQLEEEQEE--D     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY---GTEDDYQG---KPLEFGATSAALQPEEEQEE--D     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      SIEEFADVVKEQVSDLLVKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEISDDEWAAAVDEAFPLDEAEDVTE     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      SIEEFADVVKEQVSDLLVKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEVSDDEWAAAVDEAFPLDEAEDVTE     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      SIEEFADVVKEQVSDLLVKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEVSDDEWAAAVDEAFPLDEAEDVTE     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      SIEEFADVVKEQVSDLLVKLLRGMPIPDFDLDDFIDAPCYCFNAEGDASWSSTMIFSLHPVECDEECSEVEASDLEEGESECISETSTEQVDVSHEISDDEWAAAVDEAFPLDEAEDVTE     
   consensus/100%                                               plpEFAsVVt-tV.chL..l.chhs..shDLD-a..AshYhFstpG-hphuSpMhhShaPs-pDEEpu-sEtp-hE.upp.ph...uTEps..u...ps.EauAsssth...-EtE-..-     
   consensus/90%                                                EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWShATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY...GTEDDYQG...KPLEFGATSAALQP.EEQEE..D     
   consensus/80%                                                EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY...GTEDDYQG...KPLEFGATSAALQPEEEQEE..D     
   consensus/70%                                                EVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEFKLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEY...GTEDDYQG...KPLEFGATSAALQPEEEQEE..D     

                                                cov    pid 1081          .         1         .         .         .         .         :         .         .         .         .         2 1200
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      WLDDDSQQ-TVGQQDG-----S-EDNQTTTIQTIVEVQPQLEM-------------ELTPVVQ------------------TIEVNSFSGY--LKLTDNVYIKNADIVEEAKKVKPTVVV     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      SVQEEAQPVEVPVEDIAQVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRIKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLV     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      SVQEEAQPVEVPVEDIAQVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRKKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLV     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      SVQEEAQPVEVPVEDIAQVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRKKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      SVQEEAQPVEVPVEDIAQVVIADTLQETPVVSDTVEVPPQVVKLPSEPQTIQPEVKEVAPVYEADTEQTQSVTVKPKRLRIKRNVDPLSNFEHKVITECVTIVLGDAIQVAKCYGESVLV     
   consensus/100%                                               .lp--uQ..pVs.pDh.....u.p.ppTsslpshVEV.PQl.h.............ElsPVhp..................phpVsshSsa..hhlT-sVhIh.uDhlp.AKpht.oVlV     
   consensus/90%                                                WLDDDSQQ.TVGQQDG.....S.EDNQTTTIQTIVEVQPQLEM.............ELTPVVQ..................TIEVNSFSGY..LKLTDNVYIKNADIVEEAKKVKPTVVV     
   consensus/80%                                                WLDDDSQQ.TVGQQDG.....S.EDNQTTTIQTIVEVQPQLEM.............ELTPVVQ..................TIEVNSFSGY..LKLTDNVYIKNADIVEEAKKVKPTVVV     
   consensus/70%                                                WLDDDSQQ.TVGQQDG.....S.EDNQTTTIQTIVEVQPQLEM.............ELTPVVQ..................TIEVNSFSGY..LKLTDNVYIKNADIVEEAKKVKPTVVV     

                                                cov    pid 1201          .         .         .         .         :         .         .         .         .         3         .         . 1320
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQFESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      NAANTHLKHGGGIAGAINAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVN     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      NAANTHLKHGGGIAGAINAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVN     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      NAANTHLKHGGGIAGAINAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVN     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      NAANTHLKHGGGIAGAINAASKGAVQKESDEYILAKGPLQVGDSVLLQGHSLAKNILHVVGPDARAKQDVSLLSKCYKAMNAYPLVVTPLVSAGIFGVKPAVSFDYLIREAKTRVLVVVN     
   consensus/100%                                               NAANsaLKHGGGlAGAlNtAopsAhQhESD-YIhspGPLpVGsSslLpGHsLAKphLHVVGPsspttpDlpLLppsYcshNta.lllsPLlSAGIFGscPhhShchhlcps+TpVhlsV.     
   consensus/90%                                                NAANVYLKHGGGVAGALNKATNNAMQhESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
   consensus/80%                                                NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     
   consensus/70%                                                NAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVF     

                                                cov    pid 1321          .         .         :         .         .         .         .         4         .         .         .         . 1440
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      SQDVYKSLTI---------------VDIPQSLT------------------------------------------FSYDGLRGA------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      SQDVYKSLTI---------------VDIPQSLT------------------------------------------FSYDGLRGA------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      SQDVYKSLTI---------------VDIPQSLT------------------------------------------FSYDGLRGA------------------------------------     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      SQDVYKSLTI---------------VDIPQSLT------------------------------------------FSYDGLRGA------------------------------------     
   consensus/100%                                               spslYcpLs................s-IPpp.s..........................................h.Y.slpGs....................................     
   consensus/90%                                                DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
   consensus/80%                                                DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     
   consensus/70%                                                DKNLYDKLVSSFLEMKSEKQVEQKIAEIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGNLHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTA     

                                                cov    pid 1441          :         .         .         .         .         5         .         .         .         .         :         . 1560
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE-GVVD     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------IRKAKD---------Y---GFT--------------------------------------------------VFVCTDNSANTKV--LRNKGVDYTKKFLTV     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------IRKAKD---------Y---GFT--------------------------------------------------VFVCTDNSANTKV--LRNKGVDYTKKFLTV     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      ------------------IRKAKD---------Y---GFT--------------------------------------------------VFVCTDNSANTKV--LRNKGVDYTKKFLTV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      ------------------IRKAKD---------Y---GFT--------------------------------------------------VFVCTDNSANTKV--LRNKGVDYTKKFLTV     
   consensus/100%                                               ..................lRKs.s.............GaT..................................................h.VCs-spA.sps..h+.KGlchpc.hlss     
   consensus/90%                                                VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE.GVVD     
   consensus/80%                                                VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE.GVVD     
   consensus/70%                                                VVIPTKKAGGTTEMLAKALRKVPTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREMLAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQE.GVVD     

                                                cov    pid 1561          .         .         .         6         .         .         .         .         :         .         .         . 1680
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI----EFLKRGDK     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      DGVQYYCYTSKDTLDDILQQAN-KSVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAIL--MSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLNKLLHWSDQ     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      DGVQYYCYTSKDTLDDILQQAN-KSVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAIL--MSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLNKLLHWSDQ     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      DGVQYYCYTSKDTLDDILQQAN-KSVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAIL--MSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLNKLLHWSDQ     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      DGVQYYCYTSKDTLDDILQQAN-KSVGIISMPLGYVSHGLDLIQAGSVVRRVNVPYVCLLANKEQEAIL--MSEDVKLNPSEDFIKHVRTNGGYNSWHLVEGELLVQDLRLNKLLHWSDQ     
   consensus/100%                                               .GspaYhYTSKsTlssllpphN.hs.slloMPLGYVoHGLsL.pAuphhRplpVPhss.lus.-t.shh..h.pssphsPpEcFIcplphsGuYpsWphsttph.lt.....chL+huDp     
   consensus/90%                                                YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI....EFLKRGDK     
   consensus/80%                                                YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI....EFLKRGDK     
   consensus/70%                                                YGARFYFYTSKTTVASLINTLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSSKTPEEHFIETISLAGSYKDWSYSGQSTQLGI....EFLKRGDK     

                                                cov    pid 1681          .         7         .         .         .         .         :         .         .         .         .         8 1800
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      SVYYTSNPTTFHLDGEVITFDNLKT---LLS--LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV-EAFEYYHTTDPSFLGRYM     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      TICYKDSVFYVVKNSTAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFY     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      TICYKDSVFYVVKNSTAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFY     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      TICYKDSVFYVVKNSTAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFY     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      TICYKDSVFYVVKNSTAFPFETLSACRAYLDSRTTQQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFY     
   consensus/100%                                               olhYpssshhhhhsupshsF-sLps...hLs..hpp.hTIcVhsTVDslNh+T.Vls.p.TYtpQhGssahsGADlochhPcppppG+ohYlhsN.ss.cs.thhEhYtssDPoFLtRah     
   consensus/90%                                                SVYYTSNPTTFHLDGEVITFDNLKT...LLS..LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV.EAFEYYHTTDPSFLGRYM     
   consensus/80%                                                SVYYTSNPTTFHLDGEVITFDNLKT...LLS..LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV.EAFEYYHTTDPSFLGRYM     
   consensus/70%                                                SVYYTSNPTTFHLDGEVITFDNLKT...LLS..LREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRV.EAFEYYHTTDPSFLGRYM     

                                                cov    pid 1801          .         .         .         .         :         .         .         .         .         9         .         . 1920
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHXNLD-SCKRVLNVVCKTCGQQQTTLKGV     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI-ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD-SCKRVLNVVCKTCGQQQTTLKGV     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      SLKAAVHKWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGL     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      SLKAAVHKWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGSPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGL     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      SLKAAVHKWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGSPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      SLKAAVHKWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGL     
   consensus/100%                                               Shhsts+KWKhs.sstlpSlKhuDNNCYLssslhTLp.l.-lKFs.PALQcAah+t+uG-ussFhALIhAYsNpThGt.sDspchhphlht+.pLs.Ss+hVhp.hCpsCG.ppssLpGl     
   consensus/90%                                                SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD.SCKRVLNVVCKTCGQQQTTLKGV     
   consensus/80%                                                SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD.SCKRVLNVVCKTCGQQQTTLKGV     
   consensus/70%                                                SALNHTKKWKYPQVNGLTSIKWADNNCYLATALLTLQQI.ELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLD.SCKRVLNVVCKTCGQQQTTLKGV     

                                                cov    pid 1921          .         .         :         .         .         .         .         0         .         .         .         . 2040
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF---TCASEYTG-NYQCGHYKHITSKET-LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      KACCYVGVQTVEDLRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVV     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      KACCYVGVQTVEDLRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVV     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      KACCYVGVQTVEDLRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      KACCYVGVQTVEDLRARMTYVCQCGGERHRQIVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDCNVV     
   consensus/100%                                               cAshYhGs.ohEph+tthphsCpCGtptp+.lVpppoPalhhSusPsph.lppuTh...sshs.apG.phtsGHYhHhp.Kts.lhphDuuhloKoS-aKs.lTDVha.tppYooshpsV     
   consensus/90%                                                EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF...TCASEYTG.NYQCGHYKHITSKET.LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
   consensus/80%                                                EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF...TCASEYTG.NYQCGHYKHITSKET.LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     
   consensus/70%                                                EAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTF...TCASEYTG.NYQCGHYKHITSKET.LYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPV     

                                                cov    pid 2041          :         .         .         .         .         1         .         .         .         .         :         . 2160
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID-LVPNQPYPNASFDNFKFVCDNI-----KFADDLNQLTGY--KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      RYSLDGNFRTEVDPDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      RYSLDGNFRTEVDPDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      RYSLDGNFRTEVDPDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      RYSLDGNFRTEVDPDLSAFYVKDGKYFTSEPPVTYSPATILAGSVYTNSCLVSSDGQPGGDAISLSFNNLLGFDSSKPVTKKYTYSFLPKEDGDVLLAEFDTYDPIYKNGAMYKGKPILW     
   consensus/100%                                               pYpLDGshpTElDPcLssaYhKDspYFTppP.s.hsPsp.hssusasN.phVsssh.....thu.shNpLhGa..pKPso+chphoFhPc.sGDVlhh-acpYsP.aKpGAhhhtKPIlW     
   consensus/90%                                                TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID.LVPNQPYPNASFDNFKFVCDNI.....KFADDLNQLTGY..KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
   consensus/80%                                                TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID.LVPNQPYPNASFDNFKFVCDNI.....KFADDLNQLTGY..KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     
   consensus/70%                                                TYKLDGVVCTEIDPKLDNYYKKDNSYFTEQPID.LVPNQPYPNASFDNFKFVCDNI.....KFADDLNQLTGY..KKPASRELKVTFFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVW     

                                                cov    pid 2161          .         .         .         2         .         .         .         .         :         .         .         . 2280
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK--DVLECNVKTTEVVGD-IILKPANNSLKITEEVGHTDLMAAYVDNSSLT-IK     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      VNKASYDTNLNKFNRASLRQIFDVAPIELENKFTPLSVESTPV---------EP---PTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVL     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      VNKASYDTNLNKFNRASLRQIFDVAPIELENKFTPLSVESTPV---------EP---PTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVL     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      VNKASYDTNLNKFNRASLRQIFDVAPIELENKFTPLSVESTPV---------EP---PTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      VNKASYDTNLNKFNRASLRQIFDVAPIELENKFTPLSVESTPV---------EP---PTVDVVALQQEMTIVKCKGLNKPFVKDNVSFVADDSGTPVVEYLSKEDLHTLYVDPKYQVIVL     
   consensus/100%                                               hspsuhspsh.K.NphslRplasstPlEhpNpFssLpsEss.s.........cP....sV-ssslQp..sllcCpshsp.hVtD.l.hhssssuh.lsE.lu+pDLhshYVDsp..s.lh     
   consensus/90%                                                HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK..DVLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVDNSSLT.IK     
   consensus/80%                                                HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK..DVLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVDNSSLT.IK     
   consensus/70%                                                HVNNATNKATYKPNTWCIRCLWSTKPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQK..DVLECNVKTTEVVGD.IILKPANNSLKITEEVGHTDLMAAYVDNSSLT.IK     

                                                cov    pid 2281          .         3         .         .         .         .         :         .         .         .         .         4 2400
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVC-------FTLLLQLCTFTRST--NSRIKASMPTT---I     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVC-------FTLLLQLCTFTRST--NSRIKASMPTT---I     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRIT--NSRIKASMPTT---I     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      KPNELSRVLGLKTLATHGLAAVN---SVPWDT-----IANYAKPFLNKV-----------------VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST--NSRIKASMPTT---I     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      KDNVLSSMLRLHTVESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTAVGSCIKSVVRHLGVTKGILTGC-----FSFVKMLFMLPL--AYFSDSKLGTTEVKVSALKTAGVV     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      KDNVLSSMLRLHTVESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTAVGSCIKSVVRHLGVTKGILTGC-----FSFVKMLFMLPL--AYFSDSKLGTTEVKVSALKTAGVV     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      KDNVLSSMLRLHTVESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTAVGSCIKSVVRHLGVTKGILTGC-----FSFVKMLFMLPL--AYFSDSKLGTTEVKVSALKTAGVV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      KDNVLSSMLRLHTVESGDINVVAASGSLTRKVKLLFRASFYFKEFATRTFTATTAVGSCIKSVVRHLGVTKGILTGC-----FSFVKMLFMLPL--AYFSDSKLGTTEVKVSALKTAGVV     
   consensus/100%                                               KsN.LSphLtL+TltotslssVs...Slshcs.....hu.YhK.Fhs+s.................lusTpsIlTtC............FhL.L..shFoc.p..soclKsSh.pT...l     
   consensus/90%                                                KPNELSRVLGLKTLATHGLAAVN...SVPWDT.....IANYAKPFLNKV.................VSTTTNIVTRCLNRVChsah.hhFTLLLQLCTFTRST..NSRIKASMPTT...I     
   consensus/80%                                                KPNELSRVLGLKTLATHGLAAVN...SVPWDT.....IANYAKPFLNKV.................VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST..NSRIKASMPTT...I     
   consensus/70%                                                KPNELSRVLGLKTLATHGLAAVN...SVPWDT.....IANYAKPFLNKV.................VSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRST..NSRIKASMPTT...I     

                                                cov    pid 2401          .         .         .         .         :         .         .         .         .         5         .         . 2520
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL----LLSV---------CLG-SLIYST-----AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT-GSIPCSVCLSGLDSL     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      TGNVVKQCCTAAVDLSMDKLRRVDWKSTLRLLLMLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAYRANS-FDVPTFCANRSAMCNWCLISQDSI     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      TGNVVKQCCTAAVDLSMDKLRRVDWKSTLRLLLMLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAYRANS-FDVPTFCANRSAMCNWCLISQDSI     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      TGNVVKQCCTAAVDLSMDKLRRVDWKSTLRLLLMLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAYRANS-FDVPTFCANRSAMCNWCLISQDSI     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      TGNVVKQCCTAAVDLSMDKLRRVDWKSTLRLLLMLCTTMVLLSSVYHLYVFNQVLSSDVMFEDAQGLKKFYKEVRAYLGISSACDGLASAYRANS-FDVPTFCANRSAMCNWCLISQDSI     
   consensus/100%                                               stNsVKpssphsl-hShshL+pssapphlplllhhh....LLSs.........sLu.slhaps.....thht.lhu.LGhsShCsGhtpuYhsso.hslsTaCs.tSh.CshCL.u.DSl     
   consensus/90%                                                AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL....LLSV.........CLG.SLIYST.....AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT.GSIPCSVCLSGLDSL     
   consensus/80%                                                AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL....LLSV.........CLG.SLIYST.....AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT.GSIPCSVCLSGLDSL     
   consensus/70%                                                AKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFL....LLSV.........CLG.SLIYST.....AALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCT.GSIPCSVCLSGLDSL     

                                                cov    pid 2521          .         .         :         .         .         .         .         6         .         .         .         . 2640
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLI-----MAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLI-----MAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH--FIS----NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      THYPALKMVQTHLSHYVLNIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWL----FTHIPMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLC     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      THYPALKMVQTHLSHYVLNIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWL----FTHIPMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLC     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      THYPALKMVQTHLSHYVLNIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWL----FTHIPMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLC     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      THYPALKMVQTHLSHYVLNIDWLWFAFETGLAYMLYTSAFNWLLLAGTLHYFFAQTSIFVDWRSYNYAVSSAFWL----FTHIPMAGLVRMYNLLACLWLLRKFYQHVINGCKDTACLLC     
   consensus/100%                                               spYPuLchlQhplSpahhslshhhhshEhhLAYhLaTphF.hLhLAuhhphFFu.hula..ahS....sS.hhWL......hhPhuuhVRMY.hhAshahlhK.Y.HVlsGCpsosChhC     
   consensus/90%                                                DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH..FIS....NSWLMWLI...hpMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
   consensus/80%                                                DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH..FIS....NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     
   consensus/70%                                                DTYPSLETIQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVH..FIS....NSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMC     

                                                cov    pid 2641          :         .         .         .         .         7         .         .         .         .         :         . 2760
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN--     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      YKRNRLTRVEASTVVCGGKRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEV     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      YKRNRLTRVEASTVVCGGKRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEV     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      YKRNRLTRVEASTVVCGGKRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      YKRNRLTRVEASTVVCGGKRTFYITANGGISFCRRHNWNCVDCDTAGVGNTFICEEVANDLTTALRRPINATDRSHYYVDSVTVKETVVQFNYRRDGQPFYERFPLCAFTNLDKLKFKEV     
   consensus/100%                                               YKRNRhTRVEsoTlVsGs+RoFYlhANGGhuFC+hHNWNCVsCDThssGsTFIs-EVApDLohth+RPINsTDpSpYhVDSVTVKpsslph.ac+sGQ.hYERasLstFsNLDpL+hp..     
   consensus/90%                                                YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN..     
   consensus/80%                                                YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN..     
   consensus/70%                                                YKRNRATRVECTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRPINPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRAN..     

                                                cov    pid 2761          .         .         .         8         .         .         .         .         :         .         .         . 2880
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      --NTKVSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      --NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ-GFVDSDVE     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      CKTTTGIPEYNFIIYDSSDRGQESLARSACVYYSQVLCKSILLVDSSLVTSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVE     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      CKTTTGIPEYNFIIYDSSDRGQESLARSACVYYSQVLCKSILLVDSSLITSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVE     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      CKTTTGIPEYNFIIYDSSDRGQESLARSACVYYSQVLCKSILLVDSSLITSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVE     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      CKTTTGIPEYNFIIYDSSDRGQESLARSACVYYSQVLCKSILLVDSSLVTSVGDSSEIATKMFDSFVNSFVSLYNVTRDKLEKLISTARDGVRRGDNFHSVLTTFIDAARGPAGVESDVE     
   consensus/100%                                               ..sTps...hNhIlaDups+spES.A+SAsVYYSQlhCpsILLlDpuLlosVGDSuElAsKMFDuaVNoFsShaNVsh-KLcpLluTAcstlt+ssshcsVLoTFIsAARt.uhV-SDVE     
   consensus/90%                                                ..NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ.GFVDSDVE     
   consensus/80%                                                ..NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ.GFVDSDVE     
   consensus/70%                                                ..NTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQ.GFVDSDVE     

                                                cov    pid 2881          .         9         .         .         .         .         :         .         .         .         .         0 3000
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHSIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA---LKGGK     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      TNEIVDSVQYAHKHDIQITNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGG-     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      TNEIVDSVQYAHKHDIQITNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGG-     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      TNEIVDSVQYAHKHDIQITNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGG-     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      TNEIVDSVQYAHKHDIQITNESYNNYVPSYVKPDSVSTSDLGSLIDCNAASVNQIVLRNSNGACIWNAAAYMKLSDALKRQIRIACRKCNLAFRLTTSKLRANDNILSVRFTANKIVGG-     
   consensus/100%                                               Tp-lV-slphuHppDIplTs-ShNNYh.oYsKs-shospDLGuhIDCsAtplNt.Vh+spshAhIWNstsaMpLS-tL++QIR.As+KsNLsF+LTsuphRtssNllos+hs...lhGG.     
   consensus/90%                                                TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGGK     
   consensus/80%                                                TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGGK     
   consensus/70%                                                TKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIA...LKGGK     

                                                cov    pid 3001          .         .         .         .         :         .         .         .         .         1         .         . 3120
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      IVNNWLKQLIK--------VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ-RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      -APTWFNALRDFTLKGYVLATIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVPTTLAW     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      -APTWFNVLRDFTLKGYVLATIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVPTTLAW     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      -APTWFNVLRDFTLKGYVLATIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVPTTLAW     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      -APTWFNALRDFTLKGYVLATIIVFLCAVLMYLCLPTFSMVPVEFYEDRILDFKVLDNGIIRDVNPDDKCFANKHRSFTQWYHEHVGGVYDNSITCPLTVAVIAGVAGARIPDVPTTLAW     
   consensus/100%                                               .sssWhp.Lhc........sTllhhhsAslhYLhhPsasMs.hp.apscIlsaKslDsGlhRDlsssDpCFANKHtsFspWapp.hGGsYsNshsCPLhsAVIst.sGhhlPslPsTlhh     
   consensus/90%                                                IVNNWLKQLIK........VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ.RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
   consensus/80%                                                IVNNWLKQLIK........VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ.RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     
   consensus/70%                                                IVNNWLKQLIK........VTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQ.RGGSYTNDKACPLIAAVITREVGFVVPGLPGTILR     

                                                cov    pid 3121          .         .         :         .         .         .         .         2         .         .         .         . 3240
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDIATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI-IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      -VNNQIIFFVSRVFANTGSVCYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQE     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      -VNNQIIFFVSRVFANTGSVCYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQE     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      -VNNQIIFFVSRVFANTGSVCYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQE     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      -VNNQIIFFVSRVFANTGSVCYTPIDEIPYKSFSDSGCILPSECTMFRDAEGRMTPYCHDPTVLPGAFAYSQMRPHVRYDLYDGNMFIKFPEVVFESTLRITRTLSTQYCRFGSCEYAQE     
   consensus/100%                                               .sNsphlaFlsRVFussGslCYTP.c.I.YpshusSuClLsuECThF+DApG+.sPYCaDssVL.GuhAYpphRPcsRYsLhDGsh.IpFPpshhEuolRlspThsopYCRaGoCEhupt     
   consensus/90%                                                TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
   consensus/80%                                                TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     
   consensus/70%                                                TTNGDFLHFLPRVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVAYESLRPDTRYVLMDGSI.IQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEA     

                                                cov    pid 3241          :         .         .         .         .         3         .         .         .         .         :         . 3360
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYLFLPGVYSVIYLYLTF     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSYVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      GVCITTNGSWAIFNDHHLNRPGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATF     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      GVCITTNGSWAIFNDHHLNRPGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATF     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      GVCITTNGSWAIFNDHHLNRPGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATF     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      GVCITTNGSWAIFNDHHLNRPGVYCGSDFIDIVRRLAVSLFQPITYFQLTTSLVLGIGLCAFLTLLFYYINKVKRAFADYTQCAVIAVVAAVLNSLCICFVASIPLCIVPYTALYYYATF     
   consensus/100%                                               GVCloTsGpWsl.NDaahshPGVaCGsDhlsllpphhssLhQPIshhplosSlVhGhhlshhlThLhYYh.+h+RAFu-Yo.ssshsslhhlhs.hslChsssh.hh.ssYoslYhYhTF     
   consensus/90%                                                GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSaVVAFNTLLFLMSFTVLCLTPVYsFLPGVYSVIYLYLTF     
   consensus/80%                                                GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     
   consensus/70%                                                GVCVSTSGRWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTF     

                                                cov    pid 3361          .         .         .         4         .         .         .         .         :         .         .         . 3480
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGVMDTTSYREAACC     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV--VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      YFTNEPAFIMHVSWYIMFGPIVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNSL--TNDAYSRFLGLFNKYKYFSGAMETAAYREAAAC     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      YFTNEPAFIMHVSWYIMFGPIVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNSL--TNDAYSRFLGLFNKYKYFSGAMETAAYREAAAC     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      YFTNEPAFIMHVSWYIMFGPIVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNSL--TNDAYSRFLGLFNKYKYFSGAMETAAYREAAAC     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      YFTNEPAFIMHVSWYIMFGPIVPIWMTCVYTVAMCFRHFFWVLAYFSKKHVEVFTDGKLNCSFQDAASNIFVINKDTYAALRNSL--TNDAYSRFLGLFNKYKYFSGAMETAAYREAAAC     
   consensus/100%                                               YhTN-suFlhHlpWhlMFsPlVPhWhThsYhlshsh+HFaWhhu.a.K++V..hhsGh..soFp-AA.shFllNK-hYhtLRssl..s.stYsRaLuLaNKYKYFSGsM-TsuYREAAsC     
   consensus/90%                                                YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV..VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
   consensus/80%                                                YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV..VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     
   consensus/70%                                                YLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRV..VFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACC     

                                                cov    pid 3481          .         5         .         .         .         .         :         .         .         .         .         6 3600
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA---GNVQLRVIGHSMQNCV     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      HLAKALQTYSETGSDLLYQPPNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTL     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      HLAKALQTYSETGSDLLYQPPNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTL     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      HLAKALQTYSETGSDLLYQPPNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      HLAKALQTYSETGSDLLYQPPNCSITSGVLQSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTL     
   consensus/100%                                               HLAKALpsaSpoGSDlLYQPPpsSITSuVLQSGhhKMuaPSGcVEuCMVQVTCGohTLNGLWLDssVaCPRHVhCsu-ph.sPNY-sLLIphoNHsF.VQt...usspLRVlGHuMQssl     
   consensus/90%                                                HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA...GNVQLRVIGHSMQNCV     
   consensus/80%                                                HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA...GNVQLRVIGHSMQNCV     
   consensus/70%                                                HLAKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQA...GNVQLRVIGHSMQNCV     

                                                cov    pid 3601          .         .         .         .         :         .         .         .         .         7         .         . 3720
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      LKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVA     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      LKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVA     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      LKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVA     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      LKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVA     
   consensus/100%                                               LKLpVDsANPpTPtYpFsplpPGtsFSVLACYNGpPoGsapssMRPNaTIKGSFLsGSCGSVGash-hsslsFCYMHpMELssGsHsGosh-GshYGsFhD+QstQsthTDphhoVNVlA     
   consensus/90%                                                LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
   consensus/80%                                                LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     
   consensus/70%                                                LKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA     

                                                cov    pid 3721          .         .         :         .         .         .         .         8         .         .         .         . 3840
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      WLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQ--SVDMLAVKTGVAIEQLLYAI-QQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVS     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      WLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQ--SVDMLAVKTGVAIEQLLYAI-QQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVS     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      WLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQ--SVDMLAVKTGVAIEQLLYAI-QQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVS     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      WLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQ--SVDMLAVKTGVAIEQLLYAI-QQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQSGVRKVTYGTAHWLFATLVS     
   consensus/100%                                               WLYAAllNGstWFlp..pTolssFN.hAht.pap.hstsp...ls.LuspTGlAl.phhhul.p.L.sGhpG+pILGSshLEDEFTP.DVshQh.GVshQSuV++shhGTtHWLhhTllo     
   consensus/90%                                                WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
   consensus/80%                                                WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     
   consensus/70%                                                WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHWLLLTILT     

                                                cov    pid 3841          :         .         .         .         .         9         .         .         .         .         :         . 3960
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      SLLVLVQSTQWSLFFFFYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV----MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      TYVIILQATKFTLWNYLFETIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVI-VVKRLYNPSL     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      TYVIILQATKFTLWNYLFETIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVI-VVKRLYNPSL     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      TYVIILQATKFTLWNYLFETIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVI-VVKRLYNPSL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      TYVIILQATKFTLWNYLFETIPTQLFPLLFVTMAFVMLLVKHKHTFLTLFLLPVAICLTYANIVYEPTTPISSALIAVANWLAPTNAYMRTTH-TDIGVYISMSLVLVI-VVKRLYNPSL     
   consensus/100%                                               ohllllQuTpaoLa.ahaEsh.h.hh.hlhsh.AFsMhhVKHKHsFLsLFLLPshhslsYhNhVY.Pso.l....htlhsWLs.sss.hpsh+.pDhshYhShsllLll.ss+plYssuh     
   consensus/90%                                                SLLVLVQSTQWSLFFFhYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
   consensus/80%                                                SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     
   consensus/70%                                                SLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFLLPSLATVAYFNMVYMPASWV....MRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTARTVYDDGA     

                                                cov    pid 3961          .         .         .         0         .         .         .         .         :         .         .         . 4080
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      RRV-WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      SNFALALCSGVMWLYTYSIGEA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMT     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      SNFALALCSGVMWLYTYSIGEA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMT     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      SNFALALCSGVMWLYTYSIGEA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMT     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      SNFALALCSGVMWLYTYSIGEA-SSPIAYLVFVTTLTSDYTITVFVTVNLAKVCTYAIFAYSPQLTLVFPEVKMILLLYTCLGFMCTCYFGVFSLLNLKLRAPMGVYDFKVSTQEFRFMT     
   consensus/100%                                               pph.hsLhsslhhlYph.hGpA.spsIuhhshlholTSsYohsVhssh.LA+shsahhhtYsP.hhlshsplphIhLlYshLGahCTCYFGlFsLLNhhhRhshGVYDahVSTQEFRaMs     
   consensus/90%                                                RRV.WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
   consensus/80%                                                RRV.WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     
   consensus/70%                                                RRV.WTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMN     

                                                cov    pid 4081          .         1         .         .         .         .         :         .         .         .         .         2 4200
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ANNLTAPRNSWEAMALNFKLIGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQAT     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ANNLTAPRNSWEAMALNFKLIGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQAT     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      ANNLTAPRNSWEAMALNFKLIGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQAT     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      ANNLTAPRNSWEAMALNFKLIGIGGTPCIKVAAMQSKLTDLKCTSVVLLSVLQQLHLEANSRAWAFCVKCHNDILAATDPSEAFEKFVSLFATLMTFSGNVDLDALASDIFDTPSVLQAT     
   consensus/100%                                               upsLhsP+NSh-AhtLNhKLlGlGGpPCIKVAshQSKhoDlKCTSVVLLSVLQQL+lEusS+hWA.CVphHNDILhApDsoEAFEKhVSLhusLhohpGsVDlstLsp-hhDs.usLQAh     
   consensus/90%                                                SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
   consensus/80%                                                SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     
   consensus/70%                                                SQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDNRATLQAI     

                                                cov    pid 4201          .         .         .         .         :         .         .         .         .         3         .         . 4320
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      ASEFSSLPSYAAFATAQEAYEQAVANGDS-EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      LSEFSHLATFAELEAAQKAYQEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIP     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      LSEFSHLATFAELEAAQKAYQEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIP     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      LSEFSHLATFAELEAAQKAYQEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIP     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      LSEFSHLATFAELEAAQKAYQEAMDSGDTSPQVLKALQKAVNIAKNAYEKDKAVARKLERMADQAMTSMYKQARAEDKKAKIVSAMQTMLFGMIKKLDNDVLNGIISNARNGCIPLSVIP     
   consensus/100%                                               hSEFSpLsoaAthtsAQcAYppAhssGDo...VLKtLpKulNlAKsta-+DtAhtRKLE+MADQAMTpMYKQARuEDK+AKlsSAMQTMLFsMl+KLDNDsLNsIIsNARsGClPLslIP     
   consensus/90%                                                ASEFSSLPSYAAFATAQEAYEQAVANGDS.EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
   consensus/80%                                                ASEFSSLPSYAAFATAQEAYEQAVANGDS.EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     
   consensus/70%                                                ASEFSSLPSYAAFATAQEAYEQAVANGDS.EVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIP     

                                                cov    pid 4321          .         .         :         .         .         .         .         4         .         .         .         . 4440
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFIYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA-NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      LCASNKLRVVIPDFTVWNQVVTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNCNT-SSLAYYEPVQGRKMLM     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      LCASNKLRVVIPDFTVWNQVVTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNCNT-SSLAYYEPVQGRKMLM     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      LCASNKLRVVIPDFTVWNQVVTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNCNT-SSLAYYEPVQGRKMLM     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      LCASNKLRVVIPDFTVWNQVVTYPSLNYAGALWDITVINNVDNEIVKSSDV-VDSNENLTWPLVLECTRASTSAVKLQNNEIKPSGLKTMVVSAGQEQTNCNT-SSLAYYEPVQGRKMLM     
   consensus/100%                                               LssusKLhVVIPDassappssshsoh.YAuALW-Ip.lsssDscIVp.S-l.hDss.NLsWPLllpshRA.sSAVKLQNNElpPsuL+pMssuAGppQTsCss.suLAYYpsspGt+hlh     
   consensus/90%                                                LTTAAKLMVVIPDYNTYKNTCDGTTFsYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA.NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
   consensus/80%                                                LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA.NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     
   consensus/70%                                                LTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRA.NSAVKLQNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVL     

                                                cov    pid 4441          :         .         .         .         .         5         .         .         .         .         :         . 4560
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ALLSDNAYLKWARVEGKDG--FVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKT     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ALLSDNAYLKWARVEGKDG--FVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKT     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      ALLSDNAYLKWARVEGKDG--FVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKT     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      ALLSDNAYLKWARVEGKDG--FVSVELQPPCKFLIAGPKGPEIRYLYFVKNLNNLHRGQVLGHIAATVRLQAGSNTEFASNSSVLSLVNFTVDPQKAYLDFVNAGGAPLTNCVKMLTPKT     
   consensus/100%                                               ALLSD.t.LKWARh.tpDG..hl.sELpPPC+FlhssPKGPcl+YLYFlKsLNNLpRG.VLGplAATVRLQAGssTEhsuNSoVLShssFsVDstKAYhDalsuGGtPlTNCVKMLss+T     
   consensus/90%                                                ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
   consensus/80%                                                ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     
   consensus/70%                                                ALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHT     

                                                cov    pid 4561          .         .         .         6         .         .         .         .         :         .         .         . 4680
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV-----------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNGFAV-----------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      GTGQAITVTPEANMDQESLGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG-VSAARLTPCGTGTSTD     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      GTGIAISVKPESTADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLNESGVLL---------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      GTGIAISVKPESTADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLNESGVLL---------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      GTGIAISVKPESTADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLNRVRGSIVNARIEPCSSGLSTD     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      GTGIAISVKPESTADQETYGGASVCLYCRAHIEHPDVSGVCKYKGKFVQIPAQCVRDPVGFCLSNTPCNVCQYWIGYGCNCDSLRQAALPQSKDSNFLKRVRGSIVNARIEPCSSGLSTD     
   consensus/100%                                               GTG.AIoVpPEushDQEohGGASsCLYCRsHI-HPsspGhCchKGKaVQIPspCspDPVGFsLpNTsCsVCthWhGYGCsCDpLRpshL.pucspsFLpt.ts.................     
   consensus/90%                                                GTGQAITVTPEANMDQESaGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVsG.lssARlpPCuoGhSTD     
   consensus/80%                                                GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG.VSAARLTPCGTGTSTD     
   consensus/70%                                                GTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCG.VSAARLTPCGTGTSTD     

                                                cov    pid 4681          .         7         .         .         .         .         :         .         .         .         .         8 4800
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      VVYRAFDIY--NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      VVFRAFDICNYKAKVAGIGKYYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQN-SEVLKAILV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      VVFRAFDICNYKAKVAGIGKYYKTNTCRFVELDDQGHHLDSYFVVKRHTMENYELEKHCYDLLRDCDAVAPHDFFIFDVDKVKTPHIVRQRLTEYTMMDLVYALRHFDQN-SEVLKAILV     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                VVaRAFDIh..psKVAGhuKahKTNsCRF.EhD-psphlDSYFVVKRHThpNYphEcphYsLL+DCsAVA.HDFFhFclDtshsPHIsRQRLTcYTMhDLVYALRHFDps.s-sLKtILV     
   consensus/80%                                                VVYRAFDIY..NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     
   consensus/70%                                                VVYRAFDIY..NDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILV     

                                                cov    pid 4801          .         .         .         .         :         .         .         .         .         9         .         . 4920
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      KYGCCDVTYFENKLWFDFVENPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIE     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      KYGCCDVTYFENKLWFDFVENPSVIGVYHKLGERVRQAILNTVKFCDHMVKAGLVGVLTLDNQDLNGKWYDFGDFVITQPGSGVAIVDSYYSYLMPVLSMTDCLAAETHRDCDFNKPLIE     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                pYsCCDssYFppK.WaDFVENPslltVYtpLGERVRQAlLpTVpFCDtMhpAGlVGVLTLDNQDLNGpWYDFGDFl.TpPGSGVslVDSYYShLMPlLohTcsLsAEoHhDsDhsKPhIc     
   consensus/80%                                                TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     
   consensus/70%                                                TYNCCDDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESHVDTDLTKPYIK     

                                                cov    pid 4921          .         .         :         .         .         .         .         0         .         .         .         . 5040
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      WPLTEYDFTDYKVQLFEKYFKYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNA     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      WPLTEYDFTDYKVQLFEKYFKYWDQTYHANCVNCTDDRCVLHCANFNVLFAMTMPKTCFGPIVRKIFVDGVPFVVSCGYHYKELGLVMNMDVSLHRHRLSLKELMMYAADPAMHIASSNA     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                WsLhcYDFT-.+lpLF-+YFKYWDQTYHsNCVNChDDRClLHCANFNVLFuhshP.TsFGPlVRKIFVDGVPFVVSsGYHa+ELGlVhN.DVsLHppRLShKELhhYAADPAMHhASuNh     
   consensus/80%                                                WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     
   consensus/70%                                                WDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNL     

                                                cov    pid 5041          :         .         .         .         .         1         .         .         .         .         :         . 5160
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      FLDLRTSCFSVAALTTGLTFQTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFN     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      FLDLRTSCFSVAALTTGLTFQTVRPGNFNQDFYDFVVSKGFFKEGSSVTLKHFFFAQDGNAAITDYNYYSYNLPTMCDIKQMLFCMEVVNKYFEIYDGGCLNASEVVVNNLDKSAGHPFN     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                hLDhRToCFSVAALTsslsFQTV+PGNFNpDFYDFsVSKGFFKEGSSVpLKHFFFAQDGNAAIoDYsYYpYNLPTMCDI+QhLFshEVVsKYF-hYDGGClNAspVlVNNLDKSAGaPFN     
   consensus/80%                                                LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     
   consensus/70%                                                LLDKRTTCFSVAALTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFN     

                                                cov    pid 5161          .         .         .         2         .         .         .         .         :         .         .         . 5280
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      KFGKARVYYESMSYQEQDELFAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMP     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      KFGKARVYYESMSYQEQDELFAMTKRNVIPTMTQMNLKYAISAKNRARTVAGVSILSTMTNRQYHQKMLKSMAATRGATCVIGTTKFYGGWDFMLKTLYKDVDNPHLMGWDYPKCDRAMP     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                KaGKARlYY-SMSYp-QDtLFAhTKRNVIPThTQMNLKYAISAKNRARTVAGVSIhSTMTNRQaHQKhLKShAATRGATsVIGToKFYGGWc.MLKTlYpDV-NPHLMGWDYPKCDRAMP     
   consensus/80%                                                KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     
   consensus/70%                                                KWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMP     

                                                cov    pid 5281          .         3         .         .         .         .         :         .         .         .         .         4 5400
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      NMCRIFASLILARKHGTCCTTRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYA     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      NMCRIFASLILARKHGTCCTTRDRFYRLANECAQVLSEYVLCGGGYYVKPGGTSSGDATTAYANSVFNILQATTANVSALMGANGNKIVDKEVKDMQFDLYVNVYRSTSPDPKFVDKYYA     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                NMhRIhASLlLARKHsTCCohpcRFYRLANECAQVLSEhVhCGGuhYVKPGGTSSGDATTAYANSVFNIhQAsTANVsALhussGNKIsDK.V+shQacLY.slYRspssDscFVscaYA     
   consensus/80%                                                NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     
   consensus/70%                                                NMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYA     

                                                cov    pid 5401          .         .         .         .         :         .         .         .         .         5         .         . 5520
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      FLNKHFSMMILSDDGVVCYNSDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAY     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      FLNKHFSMMILSDDGVVCYNSDYAAKGYIAGIQNFKETLYYQNNVFMSEAKCWVETDLKKGPHEFCSQHTLYIKDGDDGYFLPYPDPSRILSAGCFVDDIVKTDGTLMVERFVSLAIDAY     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                aLpKHFSMMILSDDuVVCaNSsYAupGhlAuIpNFKpsLYYQNNVFMSEAKCWsETDLpKGPHEFCSQHThhlKpGDDhhaLPYPDPSRILuAGCFVDDIVKTDGTLMlERFVSLAIDAY     
   consensus/80%                                                YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     
   consensus/70%                                                YLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAY     

                                                cov    pid 5521          .         .         :         .         .         .         .         6         .         .         .         . 5640
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      PLTKHEDIEYQNVFWVYLQYIEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQAVGSCVVCHSQTSLRCGTCIRRPFLCCKCCYDHVIATPHKMVLSVSPYVCNAPGC     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      PLTKHEDIEYQNVFWVYLQYIEKLYKDLTGHMLDSYSVMLCGDNSAKFWEEAFYRDLYSSPTTLQAVGSCVVCHSQTSLRCGTCIRRPFLCCKCCYDHVIATPHKMVLSVSPYVCNAPGC     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                PLTKH.s.EYtsVFalYLQYIcKLac-LTGHMLD.YSVMLssDNou+aWE.tFYcshYos.TsLQAVGuCVlCpSQTSLRCGsCIRRPFLCCKCCYDHVIuTsHKhVLSVsPYVCNAPGC     
   consensus/80%                                                PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     
   consensus/70%                                                PLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGC     

                                                cov    pid 5641          :         .         .         .         .         7         .         .         .         .         :         . 5760
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      GVSDVTKLYLGGMSYFCVDHRPVCSFPLCANGLVFGLYKNMCTGSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASKQSYAIATIKEIVGERQLLLVWEAGKSKPP     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      GVSDVTKLYLGGMSYFCVDHRPVCSFPLCANGLVFGLYKNMCTGSPSIVEFNRLATCDWTESGDYTLANTTTEPLKLFAAETLRATEEASKQSYAIATIKEIVGERQLLLVWEAGKSKPP     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                sVoDVTpLYLGGMSYaChsH+PshSFPLCANG.VFGLYKNhCsGSssls-FNtlATCDWTpuGDYhLANTsTE.LKLFAAETL+ATEEs.K.SYuIATl+Ellu-RpLhLsWEsGKs+PP     
   consensus/80%                                                DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     
   consensus/70%                                                DVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKPRPP     

                                                cov    pid 5761          .         .         .         8         .         .         .         .         :         .         .         . 5880
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPILNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      LNRNYVFTGYHITKNSKVQLGEYIFERIDYSDAVSYKSSTTYKLTVGDIFVLTSHSVATLTAPTIVNQERYVKITGLYPTITVPEEFASHVANFQKSGYSKYVTVQGPPGTGKSHFAIGL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      LNRNYVFTGYHITKNSKVQLGEYIFERIDYSDAVSYKSSTTYKLTVGDIFVLTSHSVATLTAPTIVNQERYVKITGLYPTITVPEEFASHVANFQKSGYSKYVTVQGPPGTGKSHFAIGL     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                LNRNYVFTGY+lTKNSKVQlGEYhFE+hDYuDAVsY+uoTTYKLsVGDhFVLTSHoVhsLoAPTlVsQE+YV+ITGLYPhlsls-EFuSpVANaQKsGhpKYsTlQGPPGTGKSHFAIGL     
   consensus/80%                                                LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     
   consensus/70%                                                LNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGL     

                                                cov    pid 5881          .         9         .         .         .         .         :         .         .         .         .         0 6000
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHCVYIGDPAQLPAPRTLLTKG     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      AIYYPTARVVYTACSHAAVDALCEKAFKYLNIAKCSRIIPAKARVECYDRFKVNETNSQYLFSTINALPETSADILVVDEVSMCTNYDLSIINARIKAKHIVYVGDPAQLPAPRTLLTRG     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      AIYYPTARVVYTACSHAAVDALCEKAFKYLNIAKCSRIIPAKARVECYDRFKVNETNSQYLFSTINALPETSADILVVDEVSMCTNYDLSIINARIKAKHIVYVGDPAQLPAPRTLLTRG     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                AlYYPoARlVYTACSHAAVDALCEKAhKYLsIsKCSRIIPA+ARVECaD+FKVNpT.pQYlFsTlNALPEToADIlVhDElSMsTNYDLSllNARl+AKHhVYlGDPAQLPAPRTLLT+G     
   consensus/80%                                                ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     
   consensus/70%                                                ALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKG     

                                                cov    pid 6001          .         .         .         .         :         .         .         .         .         1         .         . 6120
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      TLEPENFNSVTRLMCNLGPDIFLSMCYRCPKEIVSTVSALVYNNKLLAKKELSGQCFKILYKGNVTHDASSAINRPQLTFVKNFITANPAWSKAVFISPYNSQNAVARSMLGLTTQTVDS     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      TLEPENFNSVTRLMCNLGPDIFLSMCYRCPKEIVSTVSALVYNNKLLAKKELSGQCFKILYKGNVTHDASSAINRPQLTFVKNFITANPAWSKAVFISPYNSQNAVARSMLGLTTQTVDS     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                TLEPE.FNSVsRLMpslGPDhFLuhChRCPtEIVsTVSALVYsNKLhA+K-hSuQCFKhhYKGslTHDsSSAINRPQlshV+pFlTtNPAWpKAVFISPYNSQNAVApphLGLsTQTVDS     
   consensus/80%                                                TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     
   consensus/70%                                                TLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDS     

                                                cov    pid 6121          .         .         :         .         .         .         .         2         .         .         .         . 6240
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      SQGSEYQYVIFCQTADTAHANNINRFNVAITRAQKGILCVMTSQALFESLEFTELSFTNY---KLQSQIVTGLFKDCSRETSGLSPAYAPTYVSVDDKYKTSDELCVNLNLPANVPYSRV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      SQGSEYQYVIFCQTADTAHANNINRFNVAITRAQKGILCVMTSQALFESLEFTELSFTNY---KLQSQIVTGLFKDCSRETSGLSPAYAPTYVSVDDKYKTSDELCVNLNLPANVPYSRV     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                SQGSEYpYVIFsQTs-TAHusNlNRFNVAITRAphGILClMospsLa-pLpFTpLphsph...pLQup.VTGLFKDCS+.hoGLpPs.APTalSVDsKaKTps.hss..slPtshsYpRl     
   consensus/80%                                                SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     
   consensus/70%                                                SQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRL     

                                                cov    pid 6241          :         .         .         .         .         3         .         .         .         .         :         . 6360
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      ISRMGFKLDATVPGYPKLFITREEAVRQVRSWIGFDVEGAHASRNACGTNVPLQLGFSTGVNFVVQPVGVVDTEWGNMLTGIAARPPPGEQFKHLVPLMHKGAAWPIVRRRIVQMLSDTL     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      ISRMGFKLDATVPGYPKLFITREEAVRQVRSWIGFDVEGAHASRNACGTNVPLQLGFSTGVNFVVQPVGVVDTEWGNMLTGIAARPPPGEQFKHLVPLMHKGAAWPIVRRRIVQMLSDTL     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                IShMGFKhshpVsGYPphFITREEAlRpVRuWIGFDVEGsHAoRpAsGTNlPLQLGFSTGVNhVs.PsGhVDT..ss.hotluA+PPPG-QFKHLlPLMaKGhsWslVRh+IVQMLSDTL     
   consensus/80%                                                ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     
   consensus/70%                                                ISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTL     

                                                cov    pid 6361          .         .         .         4         .         .         .         .         :         .         .         . 6480
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      DKLSDYCTFVCWAHGFELTSASYFCKIGKEQKCCMCNRRAAAYSSPLQSYACWTHSCGYDYVYNPFFVDVQQWGYVGNLATNHDRYCSVHQGAHVASNDAIMTRCLAIHSCFIERVDWDI     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      DKLSDYCTFVCWAHGFELTSASYFCKIGKEQKCCMCNRRAAAYSSPLQSYACWTHSCGYDYVYNPFFVDVQQWGYVGNLATNHDRYCSVHQGAHVASNDAIMTRCLAIHSCFIERVDWDI     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                cpLSDhssFVhWAHGFELTShpYFsKIG.EppCChCsRRAssaSos.poYACWpHShGaDYVYNPFhlDVQQWGasGNLtoNHDhYCpVHtsAHVASsDAIMTRCLAlHpCFlcRVDWsI     
   consensus/80%                                                KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     
   consensus/70%                                                KNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTI     

                                                cov    pid 6481          .         5         .         .         .         .         :         .         .         .         .         6 6600
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTAGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      EYPYISHEKKLNSCCRIVERNVVRAALLAGSFDKVYDIGNPKGIPIVDDPVVDWHYFDAQPLTRKV---QQLFYT-EDMASRFADGLCLFWNCNVPKYPNNAIVCRFDTRVHSEFNLPGC     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      EYPYISHEKKLNSCCRIVERNVVRAALLAGSFDKVYDIGNPKGIPIVDDPVVDWHYFDAQPLTRKV---QQLFYT-EDMASRFADGLCLFWNCNVPKYPNNAIVCRFDTRVHSEFNLPGC     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                EYPhIucEhKlNusCRhVp+.VV+AALLAspFshlaDIGNPKuI.hVspssV-W+aaDAQPhocKs...ppLFYo.tshus+FssGlCLFWNCNVs+YPsNuIVCRFDTRVhSphNLPGC     
   consensus/80%                                                EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     
   consensus/70%                                                EYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGC     

                                                cov    pid 6601          .         .         .         .         :         .         .         .         .         7         .         . 6720
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFIRLQSLENVA     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ-VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      DGGSLYVNKHAFHTPAYDVSAFRDLKPLPFFYYSTTPCEVHGNGSMIEDIDYVPLKSAVCITTCNLGGAVCRKHATEYREYMEAYNLVSASGFRLWCYKTFDIYNLWSTFTKVQGLENIA     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      DGGSLYVNKHAFHTPAYDVSAFRDLKPLPFFYYSTTPCEVHGNGSMIEDIDYVPLKSAVCITACNLGGAVCRKHATEYREYMEAYNLVSASGFRLWCYKTFDIYNLWSTFTKVQGLENIA     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                DGGSLYVNKHAFHTPAaDhSAFhsLK.LPFFYYSsoPCEsHGpt.hlpDIDYVPLKSAsCITtCNLGGAVCR+HAsEYR.Yh-AYNhh.uuGFpLWsYKpFDhYNLWsTFh+lQuLENlA     
   consensus/80%                                                DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ.VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     
   consensus/70%                                                DGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ.VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVA     

                                                cov    pid 6721          .         .         :         .         .         .         .         8         .         .         .         . 6840
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      FNVVKQGHFIGVEGELPVAVVNDKIFTKSGVNDICMFENKTTLPTNIAFELYAKRAVRSHPDFKLLHNLQADICYKFVLWDYERSNIYGTATIGVCKYTDIDVNSALNI------CFDIR     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      FNVVKQGHFIGVEGELPVAVVNDKIFTKSGVNDICMFENKTTLPTNIAFELYAKRAVRSHPDFKLLHNLQADICYKFVLWDYERSNIYGTATIGVCKYTDIDVNSALNI------CFDIR     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                FNVVppGHF.G.pGElPVullNsplaTKssssDlphFENKTTLPsNlAFELaAKRsl+shP-hKlLpNLtsDIshphVlWDYcRss.hthuTIGVCphTDIshpss.sI......hFDhR     
   consensus/80%                                                FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     
   consensus/70%                                                FNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGR     

                                                cov    pid 6841          :         .         .         .         .         9         .         .         .         .         :         . 6960
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYK-EGYAFEHIVYGDFSHS     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK---TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      DNGSLEKFMSTPNAIFISDRKIKKYPCMVGPDYAYFNGAIIRDSDVVKQPVKFYLYKKVNNEFIDPTECIYTQSRSCSDFLPLSDMEKDFLSFDSDVFIKKYGLENYAFEHVVYGDFSHT     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      DNGSLEKFMSTPNAIFISDRKIKKYPCMVGPDYAYFNGAIIRDSDVVKQPVKFYLYKKVNNEFIDPTECIYTQSRSCSDFLPLSDMEKDFLSFDSDVFIKKYGLENYAFEHVVYGDFSHT     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                ssGpl-hFhss.NulhIo-tplKth.s.VGPc.A.hNGshlhspsVh...spF.hYKKVss.h.p.sEshaTQSRshp-FhPhSpMEhDFLphs.D.FIc+Yt.EsYAFEHlVYGDFSHo     
   consensus/80%                                                VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK...TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     
   consensus/70%                                                VDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVK...TQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHS     

                                                cov    pid 6961          .         .         .         0         .         .         .         .         :         .         .         . 7080
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      TLGGLHLLIGLYKKQQEGHIIMEEMLKGSSTIHNYFITETNTAAFKAVCSVIDLKLDDFVMILKSQDLGVVSKVVKVPIDLTMIEFMLWCKDGQVQTFYPRLQASADWKPGHAMPSLFKV     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      TLGGLHLLIGLYKKQQEGHIIMEEMLKGSSTIHNYFITETNTAAFKAVCSVIDLKLDDFVMILKSQDLGVVSKVVKVPIDLTMIEFMLWCKDGQVQTFYPRLQASADWKPGHAMPSLFKV     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                pLGGLHLLIGLhK+.pEu.h.hE-hl.hsSTl+NYFIT-spTuu.KsVCSVIDLhLDDFV.IlKSQDLuVVSKVVKVsIDhT.IpFMLWCKDGpVpTFYP+LQuStsWpPGhAMPsLaKh     
   consensus/80%                                                QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     
   consensus/70%                                                QLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKM     

                                                cov    pid 7081          .         1         .         .         .         .         :         .         .         .         .         2 7200
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGMLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      QNVNLERCELANYKQSIPMPRGVHMNIAKYMQLCQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTK     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      QNVNLERCELANYKQSIPMPRGVHMNIAKYMQLCQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTK     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                Qph.LE+C-LtNYtpShshP+GlhMNlAKYhQLCQYLNThTLAVPhNMRVIHFGAGSDKGlAPGTuVLRQWLPTshlllDsDLN-FVSDAD.TLhGDCsTV+supphDLlISDMYDPpTK     
   consensus/80%                                                QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     
   consensus/70%                                                QRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTK     

                                                cov    pid 7201          .         .         .         .         :         .         .         .         .         3         .         . 7320
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ------------------------------------------------------------------------------------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ------------------------------------------------------------------------------------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQINGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ------------------------------------------------------------------------------------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ------------------------------------------------------------------------------------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      NVTGSNESKALFFTYLCNLINNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGT     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      NVTGSNESKALFFTYLCNLINNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGT     
   consensus/100%                                               ........................................................................................................................     
   consensus/90%                                                NVTtpN-SKthFFTYlCshIpppLALGGSVAIKITEHSWss-LYcLMG+FAWWTsFsTNsNASSSEuFLlGhNYLGp.+EpIsGhsMHANYIFWRNosPhpLSoYSLFDhSKF.LKL+GT     
   consensus/80%                                                NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     
   consensus/70%                                                NVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGT     

                                                cov    pid 7321          .         .         :         .     ] 7366
 1 ORF1AB_China_Dec2019a                     100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
 2 ORF1a_Finland_29Jan2020                    61.9%  99.6%      ----------------------------------------------     
 3 ORF1a_China-Yunnan_17Jan2020               62.1%  99.9%      ----------------------------------------------     
 4 ORF1AB_Finland_29Jan2020                   99.8%  99.8%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
 5 ORF1AB_USA-CA_27Jan2020                    99.9%  99.9%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
 6 ORF1AB_USA-Illinois_21Jan2020             100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
 7 ORF1AB_USA-WI_31Jan2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
 8 ORF1AB_USA-MA_29Jan2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
 9 ORF1AB_China-Hubei-Wuhan_23Dec2019        100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
10 ORF1AB_SouthKorea_Jan2020                 100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
11 ORF1AB_USA-IL_28Jan2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
12 ORF1AB_Sweden_2020Feb07                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
13 ORF1AB_China-Guangzhou_29Jan2020          100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
14 ORF1AB_China_11Jan2020                    100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
15 ORF1AB_USA-CA_23Jan2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
16 ORF1AB_USA-CA_22Jan2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
17 ORF1AB_China-Wuhan_30Dec2019              100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
18 ORF1AB_China-Hubei-Wuhan_01Jan2020        100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
19 ORF1AB_Taiwan_05Feb2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
20 ORF1AB_USA-TX_11Feb2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
21 ORF1AB_USA-CA_23Feb2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
22 ORF1AB_China-Guangzhou_27Jan2020          100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
23 ORF1AB_Brazil_28Feb2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
24 ORF1AB_China-Yunnan_17Jan2020             100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
25 ORF1AB_USA-AZ_22Jan2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
26 ORF1AB_Japan_2020Feb10                    100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
27 ORF1AB_China-GuangdongGuangzhou_05Feb2020 100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
28 ORF1AB_USA-CA_10Feb2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
29 ORF1AB_USA-CA_06Feb2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
30 ORF1AB_China_08Jan2020                    100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
31 ORF1AB_Nepal_2020Jan13                    100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
32 ORF1AB_Taiwan_31Jan2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
33 ORF1AB_China-Hangzhou_20Jan2020           100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
34 ORF1AB_USA-WA_25Jan2020                   100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
35 ORF1AB_Australia-Victoria_25Jan2020       100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
36 ORF1AB_China_02Jan2020                    100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
37 ORF1AB_USA_19Jan2020                      100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
38 ORF1AB_China-Shenzhen_10Jan2020           100.0% 100.0%      AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN-----     
39 ORF1a_MERSctrl_UnitedArabEmirates_2013     58.2%  31.8%      ----------------------------------------------     
40 ORF1a_MERSctrl_SaudiArabia_01May2013       58.2%  31.7%      ----------------------------------------------     
41 ORF1AB_MERSctrl_SaudiArabia_01May2013      95.9%  44.4%      PVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTDVLVNTYRKLR     
42 ORF1AB_MERSctrl_UnitedArabEmirates_2013    95.9%  44.4%      PVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTDVLVNTYRKLR     
   consensus/100%                                               ..............................................     
   consensus/90%                                                sVhpLKEuQIN-hllSLLSpG+LlIR-NsplslSoDVLVNs.....     
   consensus/80%                                                AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN.....     
   consensus/70%                                                AVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN.....     

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